| #!/usr/bin/python | |
| # coding: utf-8 | |
| # Author: LE YUAN | |
| # Date: 2020-07-23 | |
| # This python script is to obtain canonical SMILES just by chemical name using PubChem API | |
| import json | |
| import time | |
| import requests | |
| import multiprocessing as mp | |
| from multiprocessing.dummy import Pool | |
| from pubchempy import Compound, get_compounds | |
| # Small example: | |
| # results = get_compounds('aspirin', 'name') | |
| # for compound in results : | |
| # print(compound.canonical_smiles) | |
| # have a try by running 100 case | |
| # with open("../../Data/database/Kcat_sabio_clean_unisubstrate.tsv", "r", encoding='utf-8') as file : | |
| # lines = file.readlines()[1:] | |
| # substrates = [line.strip().split('\t')[2] for line in lines] | |
| # print(len(substrates)) | |
| # print(substrates[:10]) | |
| # for substrate in substrates[:100] : | |
| # print(substrate) | |
| # results = get_compounds(substrate, 'name') | |
| # print(len(results)) | |
| # if len(results) >0 : | |
| # print(results[0].canonical_smiles) | |
| # else : | |
| # print('-------------------------------------------------') | |
| name_smiles = dict() | |
| # One method to obtain SMILES by PubChem API using the website | |
| def get_smiles(name): | |
| # smiles = redis_cli.get(name) | |
| # if smiles is None: | |
| try : | |
| url = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/%s/property/CanonicalSMILES/TXT' % name | |
| req = requests.get(url) | |
| if req.status_code != 200: | |
| smiles = None | |
| else: | |
| smiles = req.content.splitlines()[0].decode() | |
| print(smiles) | |
| # redis_cli.set(name, smiles, ex=None) | |
| # print smiles | |
| except : | |
| smiles = None | |
| name_smiles[name] = smiles | |
| # Another method to retrieve SMILES by Pubchempy | |
| # def get_smiles(name): | |
| # time.sleep(0.5) | |
| # results = get_compounds(name, 'name') | |
| # # print(len(results)) | |
| # if len(results) >0 : | |
| # smiles = results[0].canonical_smiles | |
| # print(smiles) | |
| # else : | |
| # smiles = None | |
| # print(smiles) | |
| # print('-------------------------------------------------') | |
| # name_smiles[name] = smiles | |
| # To obtain SMILES for substrates using provided API by PubChem | |
| def main(): | |
| # with open('./smiles_data.json') as f: | |
| # names = json.load(f) | |
| # print(len(names)) | |
| with open("../../Data/database/Kcat_sabio_clean_unisubstrate.tsv", "r", encoding='utf-8') as file : | |
| lines = file.readlines()[1:] | |
| substrates = [line.strip().split('\t')[2] for line in lines] | |
| print(len(substrates)) # 18243 | |
| names = list(set(substrates)) | |
| print(len(names)) # 3100 | |
| # for substrate in substrates[:100] : | |
| # print(substrate) | |
| # thread_pool = mp.Pool(4) | |
| thread_pool = Pool(4) | |
| thread_pool.map(get_smiles, names) | |
| with open('../../Data/database/Kcat_sabio_smiles.json', 'w') as outfile: | |
| json.dump(name_smiles, outfile, indent=2) | |
| # # To test how many entries having SMILES for Sabio-RK database | |
| # def main(): | |
| # with open('../../Data/database/Kcat_sabio_smiles.json', 'r') as infile: | |
| # name_smiles = json.load(infile) | |
| # with open("../../Data/database/Kcat_sabio_clean_unisubstrate.tsv", "r", encoding='utf-8') as file : | |
| # lines = file.readlines()[1:] | |
| # substrates = [line.strip().split('\t')[2] for line in lines] | |
| # print(len(substrates)) # 18243 | |
| # substrate_smiles = list() | |
| # for substrate in substrates : | |
| # # print(substrate) | |
| # smiles = name_smiles[substrate] | |
| # # print(smiles) | |
| # if smiles is not None : | |
| # # print(smiles) | |
| # substrate_smiles.append(smiles) | |
| # print(len(substrate_smiles)) # 15218 have SMILES | |
| if __name__ == '__main__': | |
| main() |